This three-week experiment is now part of the laboratory curriculum
in our freshman introductory biology class. Like many other colleges
and universities across the country, we routinely follow a set of
experiments that address specific topics: the cell, mitosis and meiosis, enzymes, etc. While important and commonly fail-proof, those
lab experiments end up being described by students as “boring” or
simply in terms of “it worked or didn’t work,” without much discussion. Such fail-proof experiments prevent students from appreciating
the complexity, difficulties, and rigors of science. That is not the case
with these experiments. Students have enjoyed and learned from the
“Fruit Flies & the Gut Microbiome” project as it allows them to claim
ownership of their experiments. When experiments do not work,
students have demonstrated an honest interest in finding out why
they did not get the expected results.
Another benefit to this lab is the fact that students learn and
apply basic microbiology lab techniques such as serial dilution, bacterial enumeration, and Gram staining. As seen from the pretest and
posttest survey results (Figures 5 and 6), approximately 35% of the
students go from little or no understanding of how serial dilution is
used to enumerate bacteria to a good or great gain in their understanding of this concept. Students also demonstrated good to great
gains in their ability to perform these techniques (Figures 7 and 8).
For more challenging exercises, students could also use PCR
and 16S rRNA gene sequencing (James, 2010) in one of two ways,
depending on the level of difficulty sought and the time available.
In a simpler experiment, students could perform colony PCR or
extract DNA from bacterial isolates on the MRS plates, send the
PCR products for DNA sequencing, and then use the Ribosomal
Data Base Project ( https://rdp.cme.msu.edu/) to determine whether
their isolate is Lactobacillus sp. or some other bacterium. This simple
experiment would expose the students to a newer, commonly used
bioinformatics method of bacterial identification. A more in-depth
experiment, suggested for upper-level microbiology/molecular biol-
ogy students, would be to extract the total DNA from the mashed
flies using a commercially available kit and send the DNA out to a
sequencing lab for next-generation sequencing to determine the
16S bacterial profile of their flies. There is usually a waiting period
of about 4–6 weeks for the next-generation sequencing results to
come back, so this experiment should be started in the beginning
of the semester or continued into a second semester lab. To analyze
their results, students can compare and graph differences in OTUs
(operational taxonomic units) between samples and look for changes
in the fly microbiome that would, otherwise, be missed by plating on
selective media (C. Keler, unpublished data).
AAAS (2011). Vision and Change in Undergraduate Biology Education:
A Call to Action. Washington, DC: AAAS.
Chandler, J.A., Lang, J.M., Bhatnagar, S., Eisen, J.A. & Kopp, A. (2011).
Bacterial communities of diverse Drosophila species: ecological context
of a host–microbe model system. PLoS Genetics, 7( 9).
Clemente, J.C., Pehrsson, E.C., Blaser, M.J., Sandhu, K., Gao, Z., Wang, B. et al.
(2015). The microbiome of uncontacted Amerindians. Science
Advances, 1( 3).
Crittenden, A.N. & Schnorr, S.L. (2017). Current views on hunter-gatherer
nutrition and the evolution of the human diet. American Journal of
Physical Anthropology, 162(Supplement), 84–109.
David, L.A., Materna, A.C., Friedman, J., Campos-Baptista, M.I., Blackburn, M.
C., Perrotta, A. et al. (2014). Host lifestyle affects human microbiota on
daily timescales. Genome Biology, 15, R89.
Human Microbiome Project Consortium (2012). A framework for human
microbiome research. Nature, 486, 215–221.
Human Microbiome Project Consortium (2012). Structure, function and
diversity of the healthy human microbiome. Nature, 486, 207–214.
James, G. (2010). Universal bacterial identification by PCR and DNA
sequencing of 16S rRNA gene. In M. Schuller, T. Sloots, G. James,
C. Halliday & I. Carter (Eds.), PCR for Clinical Microbiology (pp. 209–214).
Dordrecht, The Netherlands: Springer.
Keler, C., Balutis, T., Bergen, K., Laudenslager, B. & Rubino, D. (2010). Serial
dilution simulation lab. American Biology Teacher, 72, 305–307.
Shreiner, A.B., Kao, J.Y. & Young, V.B. (2015). The gut microbiome in health
and disease. Current Opinion in Gastroenterology, 31, 69–75.
Takeuchi, Y., Chaffron, S., Salcher, M.M., Shimizu-Inatsugi, R., Kobayashi, M.J.,
Diway, B. et al. (2015). Bacterial diversity and composition in the fluid of
pitcher plants of the genus Nepenthes. Systematic and Applied
Microbiology, 38, 330–339.
Waite, D.W., Deines, P. & Taylor, M.W. (2012). Gut microbiome of the
critically endangered New Zealand parrot, the kakapo (Strigops
habroptilus). PLoS ONE, 7, e35803.
Wardeh, M., Risley, C., McIntyre, M.K., Setzkorn, C. & Baylis, M. (2015).
Database of host–pathogen and related species interactions, and their
global distribution. Scientific Data, 2, article 150049.
ELIZABETH SKENDZIC ( firstname.lastname@example.org) is an Associate
Professor and CYNTHIA KELER ( email@example.com) is a Professor,
both in the Biology Department, Delaware Valley University, 700 East Butler
Pike, Doylestown, PA, 18901.
Figure 8. Students’ posttest responses to the item “Presently, I
can. . . .”